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Aliases for NLGN3 Gene

Aliases for NLGN3 Gene

  • Neuroligin 3 2 3 5
  • Gliotactin Homolog 3 4
  • KIAA1480 4
  • HNL3 3
  • NL3 4

External Ids for NLGN3 Gene

Previous GeneCards Identifiers for NLGN3 Gene

  • GC0XP066538
  • GC0XP067842
  • GC0XP068597
  • GC0XP069231
  • GC0XP070147
  • GC0XP070281
  • GC0XP070364
  • GC0XP064183

Summaries for NLGN3 Gene

Entrez Gene Summary for NLGN3 Gene

  • This gene encodes a member of a family of neuronal cell surface proteins. Members of this family may act as splice site-specific ligands for beta-neurexins and may be involved in the formation and remodeling of central nervous system synapses. Mutations in this gene may be associated with autism and Asperger syndrome. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Oct 2009]

GeneCards Summary for NLGN3 Gene

NLGN3 (Neuroligin 3) is a Protein Coding gene. Diseases associated with NLGN3 include autism susceptibility, x-linked 1 and asperger syndrome susceptibility, x-linked 1. Among its related pathways are Cell adhesion molecules (CAMs). GO annotations related to this gene include hydrolase activity and cell adhesion molecule binding. An important paralog of this gene is CES2.

UniProtKB/Swiss-Prot for NLGN3 Gene

  • Cell surface protein involved in cell-cell-interactions via its interactions with neurexin family members. Plays a role in synapse function and synaptic signal transmission, and may mediate its effects by clustering other synaptic proteins. May promote the initial formation of synapses, but is not essential for this. May also play a role in glia-glia or glia-neuron interactions in the developing peripheral nervous system (By similarity).

Gene Wiki entry for NLGN3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NLGN3 Gene

Genomics for NLGN3 Gene

Regulatory Elements for NLGN3 Gene

Promoters for NLGN3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around NLGN3 on UCSC Golden Path with GeneCards custom track

Genomic Location for NLGN3 Gene

Chromosome:
X
Start:
71,144,823 bp from pter
End:
71,175,307 bp from pter
Size:
30,485 bases
Orientation:
Plus strand

Genomic View for NLGN3 Gene

Genes around NLGN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NLGN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NLGN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NLGN3 Gene

Proteins for NLGN3 Gene

  • Protein details for NLGN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NZ94-NLGN3_HUMAN
    Recommended name:
    Neuroligin-3
    Protein Accession:
    Q9NZ94
    Secondary Accessions:
    • B2RBK1
    • D2X2H6
    • D3DVV0
    • D3DVV1
    • Q86V51
    • Q8NCD0
    • Q9NZ95
    • Q9NZ96
    • Q9NZ97
    • Q9P248

    Protein attributes for NLGN3 Gene

    Size:
    848 amino acids
    Molecular mass:
    93895 Da
    Quaternary structure:
    • Interacts with NRXN1, NRXN2 and NRXN3. Interacts (via its C-terminus) with DLG4/PSD-95 (via PDZ domain 3) (By similarity). Homodimer, and heterodimer with NLGN1 and NLGN2 (By similarity).
    SequenceCaution:
    • Sequence=AAF71231.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAA96004.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAC11226.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for NLGN3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NLGN3 Gene

Proteomics data for NLGN3 Gene at MOPED

Post-translational modifications for NLGN3 Gene

  • Glycosylation at Asn 98 and Asn 545
  • Modification sites at PhosphoSitePlus

Other Protein References for NLGN3 Gene

Antibody Products

  • R&D Systems Antibodies for NLGN3 (Neuroligin 3/NLGN3)

No data available for DME Specific Peptides for NLGN3 Gene

Domains & Families for NLGN3 Gene

Protein Domains for NLGN3 Gene

Suggested Antigen Peptide Sequences for NLGN3 Gene

Graphical View of Domain Structure for InterPro Entry

Q9NZ94

UniProtKB/Swiss-Prot:

NLGN3_HUMAN :
  • Belongs to the type-B carboxylesterase/lipase family.
Family:
  • Belongs to the type-B carboxylesterase/lipase family.
genes like me logo Genes that share domains with NLGN3: view

No data available for Gene Families for NLGN3 Gene

Function for NLGN3 Gene

Molecular function for NLGN3 Gene

UniProtKB/Swiss-Prot Function:
Cell surface protein involved in cell-cell-interactions via its interactions with neurexin family members. Plays a role in synapse function and synaptic signal transmission, and may mediate its effects by clustering other synaptic proteins. May promote the initial formation of synapses, but is not essential for this. May also play a role in glia-glia or glia-neuron interactions in the developing peripheral nervous system (By similarity).

Gene Ontology (GO) - Molecular Function for NLGN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0042043 neurexin family protein binding ISS 15152050
genes like me logo Genes that share ontologies with NLGN3: view
genes like me logo Genes that share phenotypes with NLGN3: view

Animal Models for NLGN3 Gene

MGI Knock Outs for NLGN3:

Animal Model Products

  • Taconic Biosciences Mouse Models for NLGN3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for NLGN3 Gene

Localization for NLGN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NLGN3 Gene

Cell membrane; Single-pass type I membrane protein. Cell junction, synapse. Note=Detected at both glutamatergic and GABAergic synapses. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for NLGN3 Gene COMPARTMENTS Subcellular localization image for NLGN3 gene
Compartment Confidence
plasma membrane 4
endoplasmic reticulum 2
cytosol 1
extracellular 1
lysosome 1
mitochondrion 1
vacuole 1

Gene Ontology (GO) - Cellular Components for NLGN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030425 dendrite IEA --
GO:0045202 synapse ISS --
GO:0098794 postsynapse ISS --
genes like me logo Genes that share ontologies with NLGN3: view

Pathways & Interactions for NLGN3 Gene

SuperPathways for NLGN3 Gene

genes like me logo Genes that share pathways with NLGN3: view

Pathways by source for NLGN3 Gene

1 KEGG pathway for NLGN3 Gene

Gene Ontology (GO) - Biological Process for NLGN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002087 regulation of respiratory gaseous exchange by neurological system process ISS --
GO:0006898 receptor-mediated endocytosis ISS --
GO:0007158 neuron cell-cell adhesion ISS --
GO:0007416 synapse assembly ISS --
GO:0007612 learning IMP 12669065
genes like me logo Genes that share ontologies with NLGN3: view

No data available for SIGNOR curated interactions for NLGN3 Gene

Drugs & Compounds for NLGN3 Gene

No Compound Related Data Available

Transcripts for NLGN3 Gene

Unigene Clusters for NLGN3 Gene

Neuroligin 3:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for NLGN3 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10
SP1: - - - - -
SP2: - - -
SP3: - -
SP4: - - - -
SP5:

Relevant External Links for NLGN3 Gene

GeneLoc Exon Structure for
NLGN3
ECgene alternative splicing isoforms for
NLGN3

Expression for NLGN3 Gene

mRNA expression in normal human tissues for NLGN3 Gene

mRNA differential expression in normal tissues according to GTEx for NLGN3 Gene

This gene is overexpressed in Brain - Amygdala (x4.2).

Protein differential expression in normal tissues from HIPED for NLGN3 Gene

This gene is overexpressed in Frontal cortex (37.8), Brain (9.2), and Spinal cord (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for NLGN3 Gene



SOURCE GeneReport for Unigene cluster for NLGN3 Gene Hs.438877

mRNA Expression by UniProt/SwissProt for NLGN3 Gene

Q9NZ94-NLGN3_HUMAN
Tissue specificity: Expressed in the blood vessel walls (at protein level). Detected in throughout the brain and in spinal cord. Detected in brain, and at lower levels in pancreas islet beta cells.
genes like me logo Genes that share expression patterns with NLGN3: view

Protein tissue co-expression partners for NLGN3 Gene

- Elite partner

Primer Products

In Situ Assay Products

Orthologs for NLGN3 Gene

This gene was present in the common ancestor of animals.

Orthologs for NLGN3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NLGN3 36
  • 98 (a)
OneToOne
NLGN3 35
  • 99.88 (n)
  • 99.88 (a)
cow
(Bos Taurus)
Mammalia NLGN3 36
  • 96 (a)
OneToOne
NLGN3 35
  • 94.27 (n)
  • 99.38 (a)
dog
(Canis familiaris)
Mammalia NLGN3 35
  • 94.06 (n)
  • 99.06 (a)
NLGN3 36
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Nlgn3 36
  • 99 (a)
OneToOne
Nlgn3 16
Nlgn3 35
  • 93.29 (n)
  • 99.03 (a)
oppossum
(Monodelphis domestica)
Mammalia NLGN3 36
  • 97 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nlgn3 35
  • 92.85 (n)
  • 98.94 (a)
chicken
(Gallus gallus)
Aves NLGN3 35
  • 82.19 (n)
  • 90.93 (a)
NLGN3 36
  • 89 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NLGN3 36
  • 88 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.8772 35
tropical clawed frog
(Silurana tropicalis)
Amphibia nlgn3 35
  • 74.86 (n)
  • 87.64 (a)
zebrafish
(Danio rerio)
Actinopterygii nlgn3a 36
  • 81 (a)
OneToMany
nlgn3b 36
  • 71 (a)
OneToMany
nlgn3a 35
  • 74.59 (n)
  • 84.53 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003115 35
  • 51.45 (n)
  • 42.77 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG34139 35
  • 50.92 (n)
  • 44.31 (a)
alpha-Est1 37
  • 29 (a)
alpha-Est2 37
  • 27 (a)
alpha-Est4 37
  • 28 (a)
alpha-Est7 37
  • 27 (a)
CG10175 37
  • 28 (a)
CG10339 37
  • 28 (a)
CG3841 37
  • 29 (a)
CG5030 37
  • 41 (a)
CG6018 37
  • 31 (a)
CG6414 37
  • 28 (a)
CG7529 37
  • 26 (a)
CG8424 37
  • 27 (a)
CG9289 37
  • 28 (a)
Gli 37
  • 31 (a)
Jhe 37
  • 27 (a)
neuroligin 37
  • 33 (a)
worm
(Caenorhabditis elegans)
Secernentea B0238.7 37
  • 28 (a)
C52A10.1 37
  • 29 (a)
F07C4.12 37
  • 30 (a)
F13H6.3 37
  • 29 (a)
F15A8.6 37
  • 28 (a)
F55D10.3 37
  • 26 (a)
ges-1 37
  • 27 (a)
K11G9.1 37
  • 28 (a)
K11G9.2 37
  • 29 (a)
K11G9.3 37
  • 29 (a)
T28C12.4a 37
  • 29 (a)
T28C12.4b 37
  • 29 (a)
Y71H2AM.13 37
  • 27 (a)
Species with no ortholog for NLGN3:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NLGN3 Gene

ENSEMBL:
Gene Tree for NLGN3 (if available)
TreeFam:
Gene Tree for NLGN3 (if available)

Paralogs for NLGN3 Gene

Paralogs for NLGN3 Gene

(16) SIMAP similar genes for NLGN3 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with NLGN3: view

Variants for NLGN3 Gene

Sequence variations from dbSNP and Humsavar for NLGN3 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
VAR_015668 Asperger syndrome, X-linked, 1 (ASPGX1)
VAR_015668 Autism, X-linked 1 (AUTSX1)
VAR_068887 -
rs17854697 - 71,169,702(+) CCTCC(A/C)TCCTG intron-variant, reference, missense
rs17857400 - 71,169,801(+) GAGCC(A/G/T)GGGCC intron-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for NLGN3 Gene

Variant ID Type Subtype PubMed ID
esv1584074 OTHER Inversion 17803354
esv33082 CNV Loss 17666407
esv27208 CNV Gain 19812545

Variation tolerance for NLGN3 Gene

Residual Variation Intolerance Score: 3.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.04; 21.35% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NLGN3 Gene

HapMap Linkage Disequilibrium report
NLGN3
Human Gene Mutation Database (HGMD)
NLGN3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NLGN3 Gene

Disorders for NLGN3 Gene

MalaCards: The human disease database

(11) MalaCards diseases for NLGN3 Gene - From: OMIM, ClinVar, GeneTests, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
autism susceptibility, x-linked 1
  • autism, x-linked 1
asperger syndrome susceptibility, x-linked 1
  • asperger syndrome, x-linked, 1
autism spectrum disorder
  • pervasive development disorder
asperger syndrome
  • asperger disorder
cornelia de lange syndrome 4
  • cdls4
- elite association - COSMIC cancer census association via MalaCards
Search NLGN3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

NLGN3_HUMAN
  • Autism, X-linked 1 (AUTSX1) [MIM:300425]: A complex multifactorial, pervasive developmental disorder characterized by impairments in reciprocal social interaction and communication, restricted and stereotyped patterns of interests and activities, and the presence of developmental abnormalities by 3 years of age. Most individuals with autism also manifest moderate mental retardation. {ECO:0000269 PubMed:12669065}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
  • Asperger syndrome, X-linked, 1 (ASPGX1) [MIM:300494]: A syndrome with features similar to autism. Affected individuals exhibit qualitative impairment in social interaction, as manifest by impairment in the use of non-verbal behaviors such as eye-to-eye gaze, facial expression, body postures, and gestures, failure to develop appropriate peer relationships, and lack of social sharing or reciprocity. Patients also exhibit restricted, repetitive and stereotyped patterns of behavior, interests, and activities, including abnormal preoccupation with certain activities and inflexible adherence to routines or rituals. Asperger syndrome is primarily distinguished from autism by the higher cognitive abilities and a more normal and timely development of language and communicative phrases. {ECO:0000269 PubMed:12669065}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

Relevant External Links for NLGN3

Genetic Association Database (GAD)
NLGN3
Human Genome Epidemiology (HuGE) Navigator
NLGN3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
NLGN3
genes like me logo Genes that share disorders with NLGN3: view

No data available for Genatlas for NLGN3 Gene

Publications for NLGN3 Gene

  1. The structure and expression of the human neuroligin-3 gene. (PMID: 10767552) Philibert R.A. … Ginns E.I. (Gene 2000) 2 3 4 67
  2. A substitution involving the NLGN4 gene associated with autistic behavior in the Greek population. (PMID: 19645625) Pampanos A. … Kitsiou-Tzeli S. (Genet Test Mol Biomarkers 2009) 3 23
  3. Altered synchrony and connectivity in neuronal networks expressing an autism-related mutation of neuroligin 3. (PMID: 19406211) Gutierrez R.C. … Colicos M.A. (Neuroscience 2009) 3 23
  4. No evidence for involvement of genetic variants in the X-linked neuroligin genes NLGN3 and NLGN4X in probands with autism spectrum disorder on high functioning level. (PMID: 18189281) Wermter A.K. … Remschmidt H. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2008) 3 23
  5. Analysis of the neuroligin 4Y gene in patients with autism. (PMID: 18628683) Yan J. … Sommer S.S. (Psychiatr. Genet. 2008) 3 23

Products for NLGN3 Gene

Sources for NLGN3 Gene

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